Question: Number of sequenced positions from a BAM file
0
gravatar for rubic
22 months ago by
rubic180
United States
rubic180 wrote:

Hi,

Is there a samtools or other tool command that given a bam (and/or indexed bam) file will report the number of sites sequenced?

rna-seq samtools bam • 469 views
ADD COMMENTlink modified 22 months ago by Devon Ryan88k • written 22 months ago by rubic180
0
gravatar for Devon Ryan
22 months ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

I'm sure there are a few out there (there's probably something in picard), but it's simple enough to pipe samtools depth through awk and just quickly count things. This has the benefit of allowing you to easily filter by MAPQ and other things.

ADD COMMENTlink written 22 months ago by Devon Ryan88k
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